Literature DB >> 15240443

Determination of a unique solution to parallel proton transfer reactions using the genetic algorithm.

D Moscovitch1, O Noivirt, A Mezer, E Nachliel, T Mark, M Gutman, G Fibich.   

Abstract

Kinetic analysis of the dynamics as measured in multiequilibria systems is readily attained by curve-fitting methodologies, a treatment that can accurately retrace the shape of the measured signal. Still, these reconstructions are not related to the detailed mechanism of the process. In this study we subjected multiple proton transfer reactions to rigorous kinetic analysis, which consists of solving a set of coupled-nonlinear differential rate equations. The manual analysis of such systems can be biased by the operator; thus the analysis calls for impartial corroboration. What is more, there is no assurance that such a complex system has a unique solution. In this study, we used the Genetic Algorithm to investigate whether the solution of the system will converge into a single global minimum in the multidimensional parameter space. The experimental system consisted of proton transfer between four proton-binding sites with seven independent adjustable parameters. The results of the search indicate that the solution is unique and all adjustable parameters converge into a single minimum in the multidimensional parameter space, thus corroborating the accuracy of the manual analysis.

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Year:  2004        PMID: 15240443      PMCID: PMC1304368          DOI: 10.1529/biophysj.104.039925

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  11 in total

1.  Proton-collecting properties of bovine heart cytochrome C oxidase: kinetic and electrostatic analysis.

Authors:  Y Marantz; O Einarsdóttir O; E Nachliel; M Gutman
Journal:  Biochemistry       Date:  2001-12-18       Impact factor: 3.162

2.  Time-resolved dynamics of proton transfer in proteinous systems.

Authors:  M Gutman; E Nachliel
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

3.  Effect of buffer on kinetics of proton equilibration with a protonable group.

Authors:  M Gutman; E Nachliel; E Gershon
Journal:  Biochemistry       Date:  1985-06-04       Impact factor: 3.162

4.  Mechanism of proton entry into the cytoplasmic section of the proton-conducting channel of bacteriorhodopsin.

Authors:  S Checover; E Nachliel; N A Dencher; M Gutman
Journal:  Biochemistry       Date:  1997-11-11       Impact factor: 3.162

Review 5.  The pH jump: probing of macromolecules and solutions by a laser-induced, ultrashort proton pulse--theory and applications in biochemistry.

Authors:  M Gutman
Journal:  Methods Biochem Anal       Date:  1984

6.  Probing of the substrate binding domain of lactose permease by a proton pulse.

Authors:  E Nachliel; M Gutman
Journal:  Biochim Biophys Acta       Date:  2001-09-03

7.  Dynamics of the proton transfer reaction on the cytoplasmic surface of bacteriorhodopsin.

Authors:  S Checover; Y Marantz; E Nachliel; M Gutman; M Pfeiffer; J Tittor; D Oesterhelt; N A Dencher
Journal:  Biochemistry       Date:  2001-04-10       Impact factor: 3.162

8.  Gaugement of the inner space of the apomyoglobin's heme binding site by a single free diffusing proton. II. Interaction with a bulk proton.

Authors:  E Shimoni; E Nachliel; M Gutman
Journal:  Biophys J       Date:  1993-02       Impact factor: 4.033

9.  Rapid pH and deltamuH+ jump by short laser pulse.

Authors:  M Gutman; D Huppert
Journal:  J Biochem Biophys Methods       Date:  1979

10.  Proton transfer dynamics on the surface of the late M state of bacteriorhodopsin.

Authors:  Esther Nachliel; Menachem Gutman; Jörg Tittor; Dieter Oesterhelt
Journal:  Biophys J       Date:  2002-07       Impact factor: 4.033

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  3 in total

1.  A new platform to study the molecular mechanisms of exocytosis.

Authors:  Aviv Mezer; Esther Nachliel; Menachem Gutman; Uri Ashery
Journal:  J Neurosci       Date:  2004-10-06       Impact factor: 6.167

2.  Evaluation of the heterogeneous reactivity of the syntaxin molecules on the inner leaflet of the plasma membrane.

Authors:  Dana Bar-On; Menachem Gutman; Aviv Mezer; Uri Ashery; Thorsten Lang; Esther Nachliel
Journal:  J Neurosci       Date:  2009-09-30       Impact factor: 6.167

3.  A simple yeast-based strategy to identify host cellular processes targeted by bacterial effector proteins.

Authors:  Eran Bosis; Dor Salomon; Guido Sessa
Journal:  PLoS One       Date:  2011-11-15       Impact factor: 3.240

  3 in total

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